Method of calibrating ligand specificity

ABSTRACT

A method to determine specificity of ligand binding includes comparing a solid phase carrier first extract obtained by pre-treating a sample with a ligand-immobilized solid phase carrier and a solid phase carrier second extract obtained by treating the pretreated sample again with a ligand-immobilized solid phase carrier in terms of the proteins contained therein, and identifying a protein whose content is remarkably decreased in the second extract compared to the first extract, in order to solve 1) the problem of the solubility of subject ligand, 2) the problem of the non-specific protein-denaturing effect of the subject ligand added, and the like, in antagonism experiments in target search using an affinity resin.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a national phase of international patent applicationno. PCT/JP2004/015655, filed Oct. 15, 2004, which claims the benefit ofpatent application no. JP 2003-354503, filed Oct. 15, 2003, the entirecontent of which is incorporated herein by reference.

TECHNICAL FIELD

The present invention relates to analyzing intermolecular interactionsusing a solid phase carrier. More specifically, the present inventionrelates to selecting and purifying a molecule exhibiting a specificinteraction with a molecule to be analyzed, or to analyze a specificinteraction between molecules, by immobilizing the molecule to beanalyzed to a solid phase carrier, and measuring and analyzing theintermolecular interaction on the solid phase carrier.

BACKGROUND OF THE INVENTION

In researching target protein interactions using an affinity resin, itis important to determine whether an affinity-bound protein is specificfor a ligand or non-specific. Traditionally, to accomplish this purpose,an antagonism experiment that comprises adding a non-modified subjectligand to a starting material protein mixture in advance orsimultaneously with the addition of the affinity resin, and confirmingthe reduction or disappearance of the amount of the subject protein, hasbeen used. Hence, inhibition of the binding of the protein to theaffinity resin by the co-presence of the ligand as an antagonist hasbeen considered to be an essential condition for the determination thatthe protein is specific for the ligand. However, when applying thismethod, it is often difficult to dissolve a required amount of ligand inthe subject protein mixture. This represents representing a drawback inthat such experiments are substantially unperformable. In particular,when a pharmaceutical is the subject, which often possesses fatsolubility (in particular, orally administrable pharmaceuticals possessfat solubility to ensure membrane permeability by passive diffusion), asufficient ligand concentration cannot be achieved so that experimentalstudies of proteins found on affinity resins by antagonism experimentshave been abandoned to date. Specifically, to perform an antagonismexperiment, it is necessary to dissolve several hundred μg/ml of aligand (for example, provided that TOYO-Pearl 10 μl=1 μmol is used, inthe case of a ligand (antagonist) having a molecular weight of 500, asolubility of not less than 0.5 mg/ml is required, even when an equalamount of drug is present with the ligand on the resin) in an aqueoussolution wherein the protein is present; generally, it is difficult todissolve such a high concentration of ligand in a biological materialsolution wherein considerable amounts of various ions and solutes suchas proteins are dissolved. This limitation is a problem common not onlyto pharmaceuticals but also to compounds that exhibit interestingpharmacological action in oral administration, for example,environmental substances, toxic substances and the like, and there hasbeen a demand to overcome this limitation in the entire research intodrug discovery target search.

Also, in conventional methods, a ligand is often added in an amount notless than the amount of the ligand on the resin to secure anantagonistic effect, and this practice is a major problem of proteindenaturation due to the presence of a ligand at a high concentration ofseveral mg/ml in a biological material solution such as a lysate. Thatis, even if band disappearance due to the addition of a ligand isobserved during an antagonism experiment performed to determine thespecificity of an affinity-resin-bound protein, it is difficult todetermine whether the observation is due to antagonistic effect orderived from the inactivation of the protein by the non-specificprotein-denaturing effect of the ligand.

Therefore, there has been a method of determining the ligand specificityof a protein that binds to an affinity resin, which enables solving 1)the problem of the solubility of subject ligand, and 2) the problem ofthe non-specific protein-denaturing effect of the subject ligand added,which have been problematic in conventional antagonism experimentsdescribed above.

It is an object of the present invention to provide a method ofdetermining the ligand specificity of a protein that binds to anaffinity resin, particularly to provide a method of determining ligandspecificity wherein the solubility of ligand and the non-specificprotein-denaturing effect of the added subject ligand are at issue.

BRIEF SUMMARY OF THE INVENTION

In view of the above problems, the present inventors conducted variousinvestigations, and found that by performing a step of “pre-treatingwith a ligand-immobilized affinity resin” in place of “a step of addingan unmodified ligand directly to a protein mixture” that is performed inantagonism experiments for the conventional method, 1) the problem ofthe solubility of subject ligand, 2) the problem of the non-specificprotein-denaturing effect of the subject ligand added, and the like, canbe solved at one time. The present invention establishes a series ofmethods of determining ligand specificity.

In a sample, particularly in a biological sample, a protein thatnon-specifically binds and is adsorbed to a particular ligand ispresent, in addition to a protein that specifically binds to the ligand.Against this background, the present invention relates to a method ofdetermining the ligand specificity of various proteins that bind to aligand. The present invention is based on the new finding that a proteinthat specifically binds to a ligand has a high binding constant andpreferentially binds to a ligand-immobilized solid phase carrier.

Accordingly, the present invention relates to the following:

[1] A method of determining whether or not the binding of a moleculecapable of binding to a ligand to the ligand is specific, whichcomprises the steps shown below;

(1) a step of treating a sample with a ligand-immobilized solid phasecarrier to obtain a treated liquid, and extracting the protein boundonto the solid phase carrier to obtain a ligand-immobilized solid phasecarrier first extract,

(2) a step of treating the treated liquid obtained in the previous stepwith a ligand-immobilized solid phase carrier (another solid phasecarrier wherein the same kind of ligand as the ligand-immobilized solidphase carrier used in the previous step is immobilized) to obtain atreated liquid, and extracting the protein bound onto the solid phasecarrier to obtain a ligand-immobilized solid phase carrier secondextract,(3) a step of comparing and analyzing the proteins contained in theligand-immobilized solid phase carrier first extract and the proteinscontained in the ligand-immobilized solid phase carrier second extract,(4) a step of identifying a protein that is detected in theligand-immobilized solid phase carrier first extract, and that is notdetected in the ligand-immobilized solid phase carrier second extractor, even if detected, shows a significantly greater reduction comparedto other proteins than in the ligand-immobilized solid phase carrierfirst extract, on the basis of the analytical results obtained in thestep (3), and determining the protein to be specific for the ligand.[2] The method described in [1] above, which comprises repeating thestep (2) twice or more.[3] A method of determining whether or not the binding of a moleculecapable of binding to a ligand to the ligand is specific, whichcomprises the steps shown below;(1) a step of dividing a sample into two portions, and treating onethereof with an inert-substance-immobilized solid phase carrier toobtain a treated liquid,(2) a step of treating the treated liquid after treatment with theinert-substance-immobilized solid phase carrier, obtained in theprevious step, with a ligand-immobilized solid phase carrier (anothersolid phase carrier wherein the same kind of ligand as theligand-immobilized solid phase carrier used in the step (3) and step (4)described below is immobilized) to obtain a treated liquid, andextracting the protein bound onto the solid phase carrier to obtain aligand-immobilized solid phase carrier first extract,(3) a step of treating the remaining portion of the sample divided intotwo portions in the step (1) with a ligand-immobilized solid phasecarrier to obtain a treated liquid,(4) a step of treating the treated liquid after treatment with theligand-immobilized solid phase carrier, obtained in the previous step,with a ligand-immobilized solid phase carrier (another solid phasecarrier wherein the same kind of ligand as the ligand-immobilized solidphase carrier used in the previous step (3) is immobilized) to obtain atreated liquid, and extracting the protein bound onto the solid phasecarrier to obtain a ligand-immobilized solid phase carrier secondextract,(5) a step of comparing and analyzing the proteins contained in theligand-immobilized solid phase carrier first extract and the proteinscontained in the ligand-immobilized solid phase carrier second extract,(6) a step of identifying a protein that is detected in theligand-immobilized solid phase carrier first extract, and that is notdetected in the ligand-immobilized solid phase carrier second extractor, even if detected, shows a significantly greater reduction comparedto other proteins than in the ligand-immobilized solid phase carrierfirst extract, on the basis of the analytical results obtained in thestep (5), and determining the protein to be specific for the ligand.[4] The method described in [3] above, wherein the inert substance isstearic acid.[5] The method described in [3] above, wherein the inert substance isstructurally similar to the subject ligand, and does not possess thephysiological activity possessed by the ligand.[6] The method described in [1] or [3] above, wherein the sample is abiological sample.[7] The method described in [1] or [3] above, which further comprises astep of calculating the binding constant of the protein in the sample tothe ligand by comparison and analysis.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is a drawing schematically showing a mode of an embodiment of thepresent invention.

FIG. 2 is a drawing schematically showing a mode of an embodiment of thepresent invention.

FIG. 3 is a drawing showing that the binding of a molecule capable ofbinding to a ligand is specific (ligand: FK506). In the figure, A to Eare the results for optionally chosen proteins that were expected not tobe specific for FK506.

DETAILED DESCRIPTION OF THE INVENTION

A mode of an embodiment of the present invention is schematically shownin FIG. 1 (mode of embodiment 1). (1) A step of treating a sample with aligand-immobilized solid phase carrier to obtain a treated liquid, andextracting the protein bound onto the solid phase carrier to obtain aligand-immobilized solid phase carrier first extract.

The sample used in this step can comprise a substance that specificallybinds to the subject ligand, and comprises a plurality of substances.The sample may consist essentially of known compounds, may comprise somenovel compounds, and may consist essentially of novel compounds. In asample consisting essentially of known compounds, a mixture of purifiedproteins prepared by gene engineering using Escherichia coli and thelike, are included. A sample comprising some novel compounds include abiological sample such as blood, plasma, serum, urine, or a cell ortissue extract or lysate. In a sample consisting essentially of novelcompounds, a mixture of novel proteins whose functions and structuresare not yet known, or newly synthesized compounds and the like areincluded. When the sample is a mixture, especially when it comprisesknown compounds, the contents of these compounds in the sample mayoptionally be set at desired levels in advance, but need not always bedetermined.

Specificity of various substances such as proteins, nucleic acids,sugars, and lipids can be determined. The proteins encompass complexproteins such as glycoproteins and lipoproteins, as well as simpleproteins.

Depending on sample derivation and properties, in the method of solidphase carrier treatment described below and the like, the sample can bediluted with an appropriate buffer solution as required. The buffersolution includes but are not limited to the ones that do not adverselyaffect the specific interaction between the ligand and the targetmolecule. For example, physiological saline, phosphate buffer solution,tris-HCl buffer solution and the like are suitable, and a stabilizer, anantiseptic and the like may be added if desired.

In the present invention, the ligand to be immobilized to the solidphase carrier is not includes but is not limited to a known compound ora novel compound that will be developed in the future. Also, the ligandmay be a low-molecular compound or a high-molecular compound. Here, alow-molecular compound refers to a compound having a molecular weight ofless than about 1000; for example, an organic compound commonly usableas a pharmaceutical, a derivative thereof, and an inorganic compound aresuitable. Specifically, a compound produced by a method of organicsynthesis and the like, a derivative thereof, a naturally occurringcompound, a derivative thereof, a small nucleic acid molecule such as apromoter, various metals, and the like are suitable. Desirably, anorganic compound that can be used as a pharmaceutical, a derivativethereof, or a nucleic acid molecule is suitable. Also, in addition tothe high-molecular compound, a compound having a molecular weight of notless than about 1000, e.g., a protein, a polynucleic acid, apolysaccharide, or a combination thereof, and the like are suitable. Aprotein is desirable. These low-molecular compounds or high-molecularcompounds are commercially available if they are known compounds, or canbe obtained via steps such as of collection, production and purificationaccording to various publications. These may be of natural origin, ormay be prepared by genetic engineering, or may be obtained bysemi-synthesis and the like.

Immobilization of a ligand to a solid phase carrier can be performed inaccordance with a method commonly performed in the art. As a convenientand reliable means, a method utilizing an amide bond formation reactioncan be mentioned. This reaction can, for example, be performed accordingto “Peputido Gousei no Kiso to Jikken” (ISBN 4-621-02962-2, Maruzen, 1stedition issued in 1985). Regarding the reagents and solvents used ineach reaction, those in common use in the art can be utilized, and areselected appropriately depending on the binding reaction employed.

The solid phase carrier used in the present invention includes but isnot limited to carriers that allow a specific interaction between theligand and the target molecule and those commonly used in the art can beutilized, and the solid phase carrier is chosen appropriately dependingon the methods performed to treat the sample and prepare aligand-immobilized solid phase carrier extract. As examples of thematerial, resins (polystyrene, methacrylate resins, polyacrylamide andthe like), glass, metals (gold, silver, iron, silicon and the like) andthe like can be used. These solid phases may be of any form, and arechosen appropriately depending on the kind of the above-describedmaterial and the method performed for treating the sample and preparinga ligand-immobilized solid phase carrier extract. For example, plates,beads, thin films, threads, coils and the like can be used.

Treatment of a sample with a ligand-immobilized solid phase carrier isconveniently performed by mixing the ligand-immobilized solid phasecarrier and the sample. For example, a bead-like ligand-immobilizedsolid phase carrier is mixed with a sample (preferably liquid) at 4° C.to room temperature with gentle stirring for 30 minutes to overnight.When the sample is not liquid, it is preferably dissolved in anappropriate buffer solution and the like to make it liquid in advance asdescribed above. After the treatment, the ligand-immobilized solid phasecarrier and the sample are separated. This means of separation is alsoset forth appropriately depending on the form and material of theligand-immobilized solid phase carrier and the like; for example, when abead-like solid phase carrier is used, separation by centrifugaloperation or filtration is suitable. With respect to the conditions ofcentrifugal operation, various conditions commonly performed in the artare employed. Specifically, centrifugal operation at 4° C. to roomtemperature and 100 to 15000 g for 1 second to 10 minutes and filtrationusing a membrane of meshes that do not allow the passage of the solidphase carrier can be used. The supernatant or filtrate and the likeobtained through these operations is referred to as a treated liquid.

While obtaining a treated liquid as described above, the protein boundonto the solid phase carrier is extracted from the precipitate orresidue obtained by centrifugal operation or filtration of theligand-immobilized solid phase carrier, to yield a ligand-immobilizedsolid phase carrier extract. The ligand-immobilized solid phase carrierextract obtained by first treating the sample with theligand-immobilized solid phase carrier is referred to as“ligand-immobilized solid phase carrier first extract” for convenience.

With respect to the method of extracting the protein bound onto theligand-immobilized solid phase carrier, various methods commonlyperformed in the art can be utilized. This extraction is performed by,for example, treating the ligand-immobilized solid phase carrier with asurfactant-containing extract. Sodium dodecyl sulfate (SDS),polyoxyethylene sorbitan monolaurate (for example, trade name: Tween20), polyoxyethylene(9)octylphenyl ether (for example, trade name NP-40)and the like can be used as surfactants. As described below, when usingSDS-PAGE for protein detection, it is suitable to directly extract theprotein with an SDS-containing sample buffer for SDS-PAGE.

(2) The treated liquid obtained in the previous step (step (1)) istreated with a ligand-immobilized solid phase carrier to obtain atreated liquid, and the protein bound onto the solid phase carrier isextracted to obtain a ligand-immobilized solid phase carrier secondextract.

The ligand-immobilized solid phase carrier used in this step is anothersolid phase carrier wherein the same kind of ligand as theligand-immobilized solid phase carrier used in the previous step (step(1)) is immobilized.

Treatment of the treated liquid with the ligand-immobilized solid phasecarrier is performed in the same manner as the treatment of the samplewith the ligand-immobilized solid phase carrier performed in the step(1), and is conveniently performed by mixing the ligand-immobilizedsolid phase carrier and the treated liquid. For example, a bead-likeligand-immobilized solid phase carrier is mixed with the treated liquidat 4° C. to room temperature with gentle stirring for 30 minutes toovernight. After the treatment, the ligand-immobilized solid phasecarrier and the treated liquid are separated. This means of separationis also set forth appropriately depending on the form and material ofthe ligand-immobilized solid phase carrier and the like. For example,when a bead-like solid phase carrier is used, separation by centrifugaloperation or filtration is suitable. With respect to the conditions ofcentrifugal operation, various conditions commonly performed in the artare employed. Specifically, centrifugal operation at 4° C. to roomtemperature and 100 to 15000 g for 1 second to 10 minutes and filtrationoperation using a membrane of meshes that do not allow the passage ofthe solid phase carrier can be performed.

From the precipitate or residue obtained by centrifugal operation orfiltration operation, that is, a ligand-immobilized solid phase carrier,the protein bound onto the solid phase carrier is extracted to yield aligand-immobilized solid phase carrier extract. A ligand-immobilizedsolid phase carrier extract obtained by treating the treated liquid withthe ligand-immobilized solid phase carrier is referred to as“ligand-immobilized solid phase carrier second extract” for convenience.When this step is repeated twice or more, a plurality of portions ofligand-immobilized solid phase carrier second extract are obtaineddepending on the number of repeats. To prevent confusion in such cases,the portions may be distinguished from each other by designating asligand-immobilized solid phase carrier extract 2 a, 2 b, 2 c . . . andthe like.

The method of extracting the protein bound onto the ligand-immobilizedsolid phase carrier in this step is the same as the method performed inthe previous step (step (1)).

(3) A step of comparing and analyzing the proteins contained in theligand-immobilized solid phase carrier first extract and the proteinscontained in the ligand-immobilized solid phase carrier second extract.

This step can employ an ordinary method of protein analysis. Forexample, analysis by SDS-PAGE is convenient. By subjecting theligand-immobilized solid phase carrier first extract and theligand-immobilized solid phase carrier second extract to SDS-PAGE underthe same conditions, and comparing the electrophoretic patternsobtained, protein differences in the individual extracts can beexamined.

4) A protein that is detected in the ligand-immobilized solid phasecarrier first extract, and that is not detected in theligand-immobilized solid phase carrier second extract or, even ifdetected, shows a significantly greater reduction compared to otherproteins than in the ligand-immobilized solid phase carrier firstextract, on the basis of the analytical results obtained in the step(3), is determined to be specific for the ligand.

This step is based on the finding obtained in the invention of thisapplication that proteins of higher specificity (proteins having higherbinding constants) are more likely to be lost from the sample (ortreated liquid) during the first ligand-immobilized solid phase carriertreatment. To “show a significantly greater reduction compared to otherproteins than in the ligand-immobilized solid phase carrier firstextract” is visually determinable, and can be determined by astatistical process commonly performed in the art (for example, acomparison of overall protein content changes and the reduction rate ofthe content of a particular protein).

Furthermore, another mode of embodiment of the present invention isshown in FIG. 2. This mode of embodiment comprises a step of treatingwith a solid phase carrier wherein an inert substance is immobilized.This mode of embodiment is described below (mode of embodiment 2).

(1) A sample is divided into two portions, and treating one thereof withan inert-substance-immobilized solid phase carrier to obtain a treatedliquid.

The sample used in this step is the same as described above. The sampleis divided into two portions in advance, one of which is used in thisstep, and the remaining portion is used in step (3) described below. Forcomparison and analysis in the step (5), the portions of sample servingas the starting materials for the step (1) and the step (3) need to beidentical (that is, having the same composition), and the sample istherefore preferably divided into two portions in advance. If theligand-specific molecule is capable of binding onto theligand-immobilized solid phase carrier, the sample may be divided intotwo equal amounts of portions, and may be divided into two mutuallydifferent amounts of portions.

The inert substance immobilized onto a solid phase carrier in thepresent invention includes, for example, a substance other than theligand for which a target molecule is searched, and is a substance thatdoes not possess the physiological activity possessed by the ligand.Because the inert substance is expected to exhibit nearly the samebehavior as the ligand with regard to non-specific protein adsorption,the inert substance is more preferably a substance similar to the ligandin terms of characteristic functional group and core. For example,provided that the ligand for which a target molecule is searched is asubstance exhibiting anti-inflammatory effect, the inert substance is asubstance that does not exhibit anti-inflammatory effect, preferably astructurally similar substance with similar physicochemical properties.If the information on the structure-activity relationship of the ligandis available in advance and utilizable, it is possible to select aninert substance appropriately according to the information, and preparea solid phase carrier wherein the inert substance is immobilized.Meanwhile, if no such information is available in advance, a hydrophobicsubstance that is expected to normally produce non-specific proteinadsorption may be immobilized. As an example of a hydrophobic substance,stearic acid and the like can be used. Degree of hydrophobicity cangenerally be expressed by a hydrophobicity parameter; in the presentinvention, the hydrophobicity of “hydrophobic substance” can be definedby a partition coefficient, specifically LOGP. In calculating LOGP,CLOGP (a predicted value obtained using a software program forestimating a hydrophobicity parameter of a compound by a computer can becalculated using, for example, Corwin/Leo's program (CLOGP, DaylightChemical Information System Co., Ltd.)) and the like are convenientlyutilized, but the hydrophobicity parameter is not limited to CLOGP. Thegreater the CLOGP, the higher the hydrophobicity is. In removingnon-specific substances, the LOGP of the hydrophobic substance of thepresent invention is 4 or more, preferably 6 or more, calculated asCLOGP. If the LOGP is less than 4, no sufficient non-specific substanceremoval effect is obtained. Also, the greater the LOGP, the higher thehydrophobicity is, although a substance possessing such highhydrophobicity is suitable for achieving an object of the presentinvention, wherein the effect thereof does not increase remarkably evenif it exceeds about 20, calculated as CLOGP. From the viewpoint of theease of synthesis, the CLOGP is normally not more than 20. Also, becausethe problem resides in the non-specific interactions based onhydrophobic interactions on the solid phase carrier, degree of thehydrophobicity of “hydrophobic substance” may be defined more strictlyas the hydrophobicity in a state immobilized on the solid phase carrier,that is, for the entire hydrophobic-substance-immobilized solid phasecarrier.

The hydrophobic substance used in the present invention is not limited,as long as it possesses the above-described properties; such as forexample, it has an LOGP of 4 or more, preferably 6 or more, calculatedas CLOGP. More specifically, the hydrophobic substance is at leastselected from the group consisting of undecanoic acid, myristic acid,palmitic acid, linoleic acid, arachidonic acid, linolenic acid, oleicacid, stearic acid, 9-(naphthalen-1-yl)-nonanic acid, dodecanesulfonicacid, octadecanesulfonic acid and hexadecanesulfonic acid, preferably atleast one selected from the group consisting of myristic acid, palmiticacid, linoleic acid, arachidonic acid, linolenic acid, oleic acid,stearic acid, octadecanesulfonic acid and hexadecanesulfonic acid, andparticularly preferably stearic acid or octadecanesulfonic acid.

The above-described “hydrophobic substance” is commercially available ifit is a known substance, or can be prepared according to variouspublications. If the “hydrophobic substance” is a novel substance, itcan be prepared appropriately by utilizing various reactions in organicsynthesis commonly performed in the art.

The “inert substance” used in the present invention is also commerciallyavailable if it is a known substance, or can be prepared according tovarious publications. If the “inert substance” is a novel substance, itcan be prepared appropriately by utilizing various reactions in organicsynthesis commonly performed in the art. In the case of a novelsubstance, it is confirmed in advance not to possess the desiredphysiological activity, and preferably to be structurally similar to thetest subject ligand and have similar physicochemical properties.

With respect to the solid phase carrier for immobilizing an “inertsubstance” such as a hydrophobic substance, those available in the artcan be used suitably. As examples of the material, resins (polystyrene,methacrylate resins, polyacrylamide and the like), glass, metals (gold,silver, iron, silicon and the like) and the like can be used. Thesesolid phase carriers may be of any form, and are chosen appropriatelydepending on the kind of the above-described material and the methodlater performed to analyze intermolecular specific interactions. Forexample, plates, beads, thin films, threads, coils and the like can beused; beads consisting of a resin that simplify the subsequent operationwhen packed in a column are suitable, and metallic thin films and glassplates are also suitable.

Immobilization of an inert substance to the solid phase carrier isperformed by known methods commonly performed in the art and appropriatecombinations thereof. For example, immobilization by covalent bonds ornon-covalent bonds such as amide bonds, Schiff base formation, C—Cbonds, ester bonds, hydrogen bonds, and hydrophobic interactions can beperformed. All these are performed using materials and reactions knownin the art. Each binding is performed by utilizing a reaction commonlyperformed in the art. As a convenient and reliable means, a methodutilizing an amide bond formation reaction can be mentioned. Thisreaction can, for example, be performed according to “Peputido Gousei noKiso to Jikken” (ISBN 4-621-02962-2, Maruzen, 1st edition issued in1985). Regarding the reagents and solvents used in each reaction, thosein common use in the relevant field can be utilized, and are chosenappropriately depending on the binding reaction employed. Whether or notthe hydrophobic substance has been immobilized to the solid phasecarrier can, for example, be confirmed from the reaction rate determinedby a quantification (for example, the ninhydrin test) of amino groups onthe solid phase carrier surface before and after the reaction.

Treatment of a sample with an inert-substance-immobilized solid phasecarrier is conveniently performed by mixing theinert-substance-immobilized solid phase carrier and the sample. Forexample, a bead-like inert-substance-immobilized solid phase carrier ismixed with a sample (preferably liquid) at 4° C. to room temperaturewith gentle stirring for 30 minutes to overnight. When the sample is notliquid, it is preferably dissolved in an appropriate buffer solution andthe like to make it liquid in advance as described above. After thetreatment, the inert-substance-immobilized solid phase carrier and thesample are separated. This means of separation is also set forthappropriately depending on the form and material of theinert-substance-immobilized solid phase carrier and the like. Forexample, when a bead-like solid phase carrier is used, separation bycentrifugal operation or filtration is suitable. With respect to theconditions of centrifugal operation, various conditions commonlyperformed in the art are employed. Specifically, centrifugal operationat 4° C. to room temperature and 100 to 15000 g for 1 second to 10minutes and filtration operation using a membrane of meshes that do notallow the passage of the solid phase carrier can be performed. Thesupernatant or filtrate obtained through these treatments is referred toas a treated liquid. Note that although the method and procedures forthe above-described treatment can be performed appropriately asdescribed above, it is preferable, from the viewpoint of comparison,that they be performed under the same conditions using the same methodand procedures as the treatment of ligand-immobilized solid phasecarrier and sample (or treated liquid) described below.

(2) The treated liquid after treatment with theinert-substance-immobilized solid phase carrier, obtained in theprevious step (step (1)), is treated with a ligand-immobilized solidphase carrier to obtain a treated liquid, and the protein bound onto thesolid phase carrier is extracted to obtain a ligand-immobilized solidphase carrier first extract.

The ligand-immobilized solid phase carrier used in this step is anothersolid phase carrier wherein the same kind of ligand as theligand-immobilized solid phase carrier used in the steps described below(step (3) and step (4)) is immobilized.

Treatment of the treated liquid with a ligand-immobilized solid phasecarrier can be performed in the same manner as the treatment of thesample with the inert-substance-immobilized solid phase carrierperformed in the step (1). After the treatment, the protein bound ontothe solid phase carrier is extracted to yield a ligand-immobilized solidphase carrier first extract. This procedure can also be performed usingthe same conditions and procedures as those described in detail in themode of an embodiment 1.

(3) A step of treating the sample with a ligand-immobilized solid phasecarrier yields a treated liquid.

The sample used in this step is the remaining portion of the sampledivided into two portions in the step (1) above.

The ligand-immobilized solid phase carrier used in this step is anothersolid phase carrier wherein the same kind of ligand as theligand-immobilized solid phase carrier used in the step (2) isimmobilized, and can be prepared in the same manner as the“ligand-immobilized solid phase carrier” described in detail in the modeof embodiment 1. Also, treatment of the sample with theligand-immobilized solid phase carrier and recovery of the treatedliquid can also be performed in the same manner as the treatmentperformed in the above-described mode of embodiment 1.

(4) The treated liquid after treatment with the ligand-immobilized solidphase carrier, obtained in the previous step (step (3)), is treated witha ligand-immobilized solid phase carrier (another solid phase carrierwherein the same kind of ligand as the ligand-immobilized solid phasecarrier used in the previous step (3) is immobilized) to obtain atreated liquid, and the protein bound onto the solid phase carrier isextracted to obtain a ligand-immobilized solid phase carrier secondextract.

A series of operations such as treatment of the treated liquid with theligand-immobilized solid phase carrier, recovery of the treated liquidand extraction of the protein bound to the solid phase carrier to yielda ligand-immobilized solid phase carrier second extract, are performedin accordance with the above-described mode of embodiment 1.

(5) A step of comparing and analyzing the proteins contained in theligand-immobilized solid phase carrier first extract and the proteinscontained in the ligand-immobilized solid phase carrier second extractis performed.

This step can employ an ordinary method of protein analysis. Forexample, analysis by SDS-PAGE is convenient. By subjecting theligand-immobilized solid phase carrier extract 1 and theligand-immobilized solid phase carrier extract 2 to SDS-PAGE under thesame conditions, and comparing the electrophoretic patterns obtained,protein differences in the individual extracts can be examined.

(6) A protein that is detected in the ligand-immobilized solid phasecarrier extract 1, and that is not detected in the ligand-immobilizedsolid phase carrier extract 2 or, even if detected, shows asignificantly greater reduction compared to other proteins than in theligand-immobilized solid phase carrier extract 1, on the basis of theanalytical results obtained in the step (5), is determined to bespecific for the ligand.

This step, as in the mode of embodiment 1, is based on the findingobtained in the invention of this application that proteins of higherspecificity (proteins having higher binding constants) are more likelyto be removed from the sample (or treated liquid) during the firstligand-immobilized solid phase carrier treatment. That is, even when thesample is treated with an inert-substance-immobilized solid phasecarrier in advance, the ligand-specific protein is not removed from thesample. To the contrary, the ratio of ligand-specific protein in thesample increases (the non-specific proteins in the sample are removed bytreatment with inert-substance-immobilized solid phase carrier).Meanwhile, when pretreatment with an inert-substance-immobilized solidphase carrier is not performed, as is evident from the mode ofembodiment 1, the first ligand-immobilized solid phase carrier treatmentcauses the ligand-specific protein to be removed from the sample (thatis, the ligand-specific protein binds to the immobilized solid phasecarrier used for the treatment, hence the ligand-specific protein iscontained at high concentrations in the ligand-immobilized solid phasecarrier extract obtained after the first ligand-immobilized solid phasecarrier treatment).

To “show a significantly greater reduction compared to other proteinsthan in the ligand-immobilized solid phase carrier extract 1” isvisually determinable, and can be determined by a statistical processcommonly performed in the art (for example, a comparison of overallprotein content changes and the reduction rate of the content of aparticular protein).

When a more quantitative determination is required in determiningwhether or not a particular protein is ligand-specific using the methodof the present invention, a step of calculating the binding constant ofthe protein to the ligand may be included in the above-described seriesof steps.

For a method of calculating the binding constant, a method commonlyperformed in the art can be used. For example, ELISA experiments using alabeled ligand, experiments using BIACORE (see Analytical Chemistry(1999), 71, 777-790 by Whiteside et al. and the like) and the like, andthe like can be performed.

EXAMPLES

The present invention is hereinafter described in more detail by thefollowing examples, which, however, are not to be construed as limitingthe scope of the present invention. Also, the individual compounds,reagents and the like used are commercially available or can be preparedon the basis of published reports and the like unless otherwise stated.

Preparation of Ligand-Immobilized Solid Phase Carrier Production Example1 Synthesis of17-allyl-14-(tert-butyl-dimethyl-silanyloxy)-1-hydroxy-12-{2-[4-(7-(tert-butyl-dimethyl-silanyloxy-carbonyl)heptanoyl-oxy)-3-methoxy-cyclohexyl]-1-methyl-vinyl}-23,25-dimethoxy-13,19,21,27-tetramethyl-11,28-diox-4-aza-tricyclo[22.3.1.0^(4,9)]octacos-18-ene-2,3,10,16-tetraone

A mixture of17-allyl-14-(tert-butyl-dimethyl-silanyloxy)-1-hydroxy-12-[2-(4-hydroxy-3-methoxy-cyclohexyl)-1-methyl-vinyl]-23,25-dimethoxy-13,19,21,27-tetramethyl-11,28-diox-4-aza-tricyclo[22.3.1.0^(4,9)]octacos-18-ene-2,3,10,16-tetraone(FK506; 138 mg, 0.15 mmol),O-mono(tert-butyl-dimethyl-silanyl)octanedioic acid (86.7 mg, 0.218mmol), dimethylaminopyridine (DMAP; 16.5 mg, 0.098 mmol),1-[3-(dimethylamino)propyl]-3-ethylcarbodiimide hydrochloride (EDC/HCl;69.1 mg, 0.261 mmol) and methylene chloride (CH₂Cl₂; 1 ml) was stirredat room temperature for 1.5 hours. The reaction product was poured overan ethyl acetate-water mixed liquid and extracted. The organic phaseobtained was washed with water and saline, after which it was dried withmagnesium sulfate (MgSO₄). After the MgSO₄ was separated by filtration,concentration under reduced pressure was conducted. The residue thusobtained was purified using a silica gel column (eluted with 20% AcOEt(in n-hexane)) to yield the desired17-allyl-14-(tert-butyl-dimethyl-silanyloxy)-1-hydroxy-12-{2-[4-(7-(tert-butyl-dimethyl-silanyloxy-carbonyl)heptanoyl-oxy)-3-methoxy-cyclohexyl]-1-methyl-vinyl}-23,25-dimethoxy-13,19,21,27-tetramethyl-11,28-diox-4-aza-tricyclo[22.3.1.0^(4,9)]octacos-18-ene-2,3,10,16-tetraone(44 mg, 24.6%).

¹H-NMR (CDCl₃) δ: −0.1-0.1 (12H, m), 0.7-2.6 (47H, m), 0.85 and 0.86(18H, s), 1.50 (3H, s), 1.63 (3H, s), 2.75 (1H, m), 3.31 (3H, s), 3.35(3H, s), 3.39 (3H, s), 4.05 (1H, m), 3.0-4.4 (6H), 4.5-5.8 (9H, m).

Production Example 2 Synthesis of17-allyl-1,14-di-hydroxy-12-{2-[4-(7-carboxy-heptanoyl-oxy)-3-methoxy-cyclohexyl]-1-methyl-vinyl}-23,25-dimethoxy-13,19,21,27-tetramethyl-11,28-dioxa-4-aza-tricyclo[22.3.1.0^(4,9)]octacos-18-ene-2,3,10,16-tetraone

To a mixture of the17-allyl-14-(tert-butyl-dimethyl-silanyloxy)-1-hydroxy-12-{2-[4-(7-(tert-butyl-dimethyl-silanyloxy-carbonyl)heptanoyl-oxy)-3-methoxy-cyclohexyl]-1-methyl-vinyl}-23,25-dimethoxy-13,19,21,27-tetramethyl-11,28-dioxa-4-aza-tricyclo[22.3.1.0^(4,9)]octacos-18-ene-2,3,10,16-tetraoneprepared in Production Example 1 (44 mg, 0.037 mmol) and acetonitrile(0.88 ml), 46 to 48% aqueous hydrogen fluoride (HF) (0.12 ml) was gentlyadded; this was followed by overnight stirring at room temperature. Thereaction product was poured over an ethyl acetate-water mixed liquid andextracted. The organic phase obtained was washed with water and saline,after which it was dried with magnesium sulfate (MgSO₄). After the MgSO₄was separated by filtration, concentration under reduced pressure wasconducted. The residue thus obtained was purified using a silica gelcolumn (5% methanol (in chloroform)) to yield the desired17-allyl-1,14-di-hydroxy-12-{2-[4-(7-carboxy-heptanoyl-oxy)-3-methoxy-cyclohexyl]-1-methyl-vinyl}-23,25-dimethoxy-13,19,21,27-tetramethyl-11,28-dioxa-4-aza-tricyclo[22.3.1.0^(4,9)]octacos-18-ene-2,3,10,16-tetraone(14.2 mg, 40%).

¹H-NMR (CDCl₃) δ: 0.7-2.6 (47H, m), 1.50 (3H, s), 1.63 (3H, s), 2.75(1H, m), 3.31 (3H, s), 3.35 (3H, s), 3.39 (3H, s), 4.05 (1H, m), 3.0-4.4(6H), 4.5-5.8 (11H, m). MS (m/z): 960 (M⁺)

Production Example 3 Synthesis of FK506-Bound TOYO-Pearl ResinTOYO-Pearl Resin; TSKgel AF-Amino

A mixture of the17-allyl-1,14-di-hydroxy-12-{2-[4-(7-carboxy-heptanoyl-oxy)-3-methoxy-cyclohexyl]-1-methyl-vinyl}-23,25-dimethoxy-13,19,21,27-tetramethyl-11,28-dioxa-4-aza-tricyclo[22.3.1.0^(4,9)]octacos-18-ene-2,3,10,16-tetraoneprepared in Production Example 2 (38.4 mg, 0.04 mmol), TOYO-Pearl resin(TSKgel AF-amino, 100 μl, free amino group (available amino group)content 0.01 mmol; manufactured by Tosoh Corporation), EDC/HCl (9.2 mg,0.048 mmol), 1-hydroxybenzotriazole (HOBt; 6.5 mg, 0.048 mmol) anddimethylformamide (DMF; 1 ml) was stirred at room temperature for 6hours. The reaction end point was confirmed when no residual aminogroups became visually observable by the ninhydrin reaction. Thereaction rate was calculated to be about 24% (estimated ligandconcentration=24 μmol/ml). After confirmation of completion of thereaction, the resin was washed with DMF five times. Acetic anhydride(100 μl) and DMF (400 μl) were added thereto, and this was followed bystirring at room temperature for 1 hour. Subsequently, the resin wasthoroughly washed with DMF, and the FK506-bound TOYO-Pearl resinobtained was used in the binding experiments described below.

Preparation of Hydrophobic-Substance-Immobilized Solid Phase CarrierProduction Example 4 Synthesis of Stearic-Acid-Immobilized Resin[TOYO+Stearic Acid]

Stearic acid was immobilized to TOYO-Pearl resin (TSKgel AF-amino). To100 μl of the TOYO-Pearl resin, stearic acid (11.38 mg, 0.04 mmol)dissolved in a mixed solvent of DMF (0.25 ml) and dichloromethane (0.25ml) was added; benzotriazol-1-yl-oxy-tris-pyrrolidino-phosphoniumhexafluorophosphate (PyBOP; 26 mg, 0.05 mmol) andN,N-diisopropylethylamine (17 μl, 0.10 mmol) were further added, andthis was followed by shaking at room temperature for 4 hours. Aftercompletion of the reaction, the resin was thoroughly washed with DMF,after which the percent condensation yield was determined by theninhydrin test (about 91%).

Example 1 (1-1) Preparation of Lysate

The rat brain (2.2 g) was mixed in a mixture A (0.25 M sucrose, 25 mMTris buffer (pH 7.4), 22 ml) and prepared as a homogenate, which wasthen centrifuged at 9500 rpm for 10 minutes. The centrifugal supernatantwas collected and further centrifuged at 50000 rpm for 30 minutes. Thesupernatant thus obtained was used as the lysate. Note that allexperiments were performed at 4° C. or on ice.

(1-2) Binding Experiments Invention of this Application

Lysate-binding experiments were performed per the procedures shown belowusing the FK506-bound affinity resin synthesized in Production Example 3and the stearic-acid-immobilized resin prepared in Production Example 4.Note that the lysate was used after being diluted with the mixture A ata dilution rate of ½.

Each resin (10 μl) and the lysate (1 ml) were gently shaken at 4° C. forabout 1 hour. Thereafter, centrifugal operation was performed, and eachsupernatant was collected carefully. Then, each supernatant was againmixed with a fresh supply of the FK506-bound resin (10 μl). After themixture was gently stirred for about 3 hours, centrifugal operation wasperformed, and the supernatant was removed. The FK506-bound resinobtained was gently washed with the mixture A about 5 times to removesubstances other than the protein bound onto the resin to the maximumpossible extent.

To each FK506-bound resin thus obtained, 25 μl of a loading buffer forSDS (nakalai cat. NO=30566-22, sample buffer solution forelectrophoresis with 2-ME (2-mercaptoethanol) (2×) for SDS PAGE) wasadded; this was followed by stirring at 25° C. for 10 minutes. Thesample solution thus obtained was separated using a commerciallyavailable SDS gel (BioRad readyGel J, 15% SDS, cat. NO=161-J341), andthe SDS gel was analyzed.

As a result, compared to the first resin treatment performed with thestearic-acid-immobilized resin, the treatment with the FK506-bound resinshowed that the band of FKBP12, which is considered to specifically bindonto the FK506-bound resin, decreased evidently and antagonism wasobserved.

Note that this result was very similar to the result from ordinaryexperiments (conventional method) described below.

(1-3) Binding Experiments Conventional Method

Binding experiments were performed by a conventional method using theFK506-bound affinity resin synthesized in Production Example 3. Notethat the same lysate as prepared in Example 2 was used in dividedportions.

Two portions of the FK506-bound affinity resin synthesized in ProductionExample 3 (10 μl, FK506 content about 0.24 μmol) were provided; oneportion was mixed with lysate (1 ml), 10 μl of DMSO was added (to ensurethe same conditions as the experiments described below), and the mixturewas gently shaken at 4° C. for about 1 hour. The lysate used for theother portion was obtained by adding 10 μl (0.35 μmol, about 1.5 timesthe amount of ligand on the resin) of a solution of FK506 (2.83 mg)dissolved in 100 μl of DMSO in advance before mixing with the resin, andgently stirring the solution for 1 hour. Note that a prior survey hadconfirmed that the addition of these amounts of DMSO and FK506 did notcause protein denaturation or aggregation like those described above.After each mixture was gently stirred for about 3 hours, centrifugaloperation was performed, and the supernatant was removed. TheFK506-bound resin obtained was washed carefully with the mixture A about5 times to remove substances other than the protein bound onto the resinto the maximum possible extent.

To each FK506-bound resin thus obtained, 25 μl of a loading buffer forSDS (nakalai cat. NO=30566-22, sample buffer solution forelectrophoresis with 2-ME (2-mercaptoethanol) (2×) for SDS PAGE) wasadded, and this was followed by stirring at 25° C. for 10 minutes. Thesample solution thus obtained was separated using a commerciallyavailable SDS gel (BioRad readyGel J, 15% SDS, cat. NO=161-J341), andthe SDS gel was analyzed.

As a result, the band of FKBP12, which is considered to specificallybind onto the resin, disappeared when the antagonist FK506 was added inadvance, and antagonism was observed.

(1-4) Binding Experiments Invention of this Application

Note that the same results as “(1-2) Binding experiments” above can alsobe obtained with the procedures shown below.

Lysate-binding experiments were performed using the FK506-bound affinityresin synthesized in Production Example 3 per the procedures shownbelow. Note that the lysate was used after being diluted with themixture A at a dilution rate of ½.

The resin (10 μl) and the lysate (1 ml) were gently shaken at 4° C. forabout 1 hour. Thereafter, centrifugal operation was performed, and eachsupernatant was collected carefully. At this time, the separatedFK506-bound resin was kept to stand at 4° C. as the first bindingexperiment resin. Then, each supernatant was again mixed with a freshsupply of the FK506-bound resin (10 μl). After the mixture was gentlystirred for about 3 hours, centrifugal operation was performed, and thesupernatant was removed. Subsequently, the FK506-bound resin obtained inthe second binding experiment and the resin obtained in the firstbinding experiment were gently washed with the mixture A about 5 timesto remove substances other than the protein bound onto the resin to themaximum possible extent. To each FK506-bound resin thus obtained, 25 μlof a loading buffer for SDS (nakalai cat. NO=30566-22, sample buffersolution for electrophoresis with 2-ME (2-mercaptoethanol) (2×) for SDSPAGE) was added, and this was followed by stirring at 25° C. for 10minutes. The sample solution thus obtained was separated using acommercially available SDS gel (BioRad readyGel J, 15% SDS, cat.NO=161-J341), and the SDS gel was analyzed.

As a result, on the resin obtained in the first binding experiment,nearly the same results as the results from the stearic-acid-immobilizedresin treatment in “(1-2) Binding experiments” above were obtained, andfrom the resin obtained in the second binding experiment, nearly thesame results as the results from the FK506-bound resin treatment in“(1-2) Binding experiments” above were obtained. Note that these resultswere very similar to the results described in “(1-2) Binding experiments(invention of this application)” and “(1-3) Binding experiments(conventional method)” above. The results from a total of up to sixrepeats of the procedure described in (1-4) are shown in FIG. 3. Asshown in FIG. 3, a band of FKBP12, which is known to specifically bindto FK506, which was used as the ligand, was present only after the firstoperation and not at all present after the second operation and beyond.Also, the binding amounts of other proteins considered to benon-specific proteins, such as tubulin and actin, were nearly constantirrespective of the number of repeats of the operation. In target searchusing an affinity resin, antagonism experiments play an important rolein confirming determining the specificity of the bands observed. Theinvention of this application provides one technique for antagonismexperiments, which is free of the problem of the solubility of subjectligand, that has conventionally been a matter of concern, and which isassociated with less problems of the non-specific protein denaturingeffect by the subject ligand to be added. This technique is consideredto serve as a basic technology for research into affinity resins.

Preferred embodiments of this invention are described herein, includingthe best mode known to the inventors for carrying out the invention. Itshould be understood that the illustrated embodiments are exemplaryonly, and should not be taken as limiting the scope of the invention.The use of any and all examples, or exemplary language (e.g., “such as”)provided herein, is intended merely to better illuminate the inventionand does not pose a limitation on the scope of the invention unlessotherwise claimed. No language in the specification should be construedas indicating any non-claimed element as essential to the practice ofthe invention.

All references, including publications, patent applications, andpatents, cited herein are hereby incorporated by reference to the sameextent as if each reference were individually and specifically indicatedto be incorporated by reference and were set forth in its entiretyherein.

1. A method of determining whether or not the binding of a targetmolecule to a ligand is specific, the method comprises: (i) dividing asample containing the target molecule into first and second portions,and treating the first portion with a solid phase carrier comprising animmobilized inert substance to obtain a first once-treated liquid, (ii)treating the first once-treated liquid with a solid phase carriercomprising an immobilized ligand that binds the target molecule toobtain a first twice-treated liquid, (iii) extracting the targetmolecule bound to the ligand immobilized on the solid phase carrier in(ii) to obtain a first extract, (iv) treating the second portion with asolid phase carrier comprising the immobilized ligand as in step (ii)that binds the target molecule to obtain a second once-treated liquid,(v) treating the second once-treated liquid with a solid phase carriercomprising the immobilized ligand as in step (iv) that binds the targetmolecule to obtain a second twice-treated liquid, (vi) extracting thetarget molecule bound to the ligand immobilized on the solid phasecarrier in (v) to obtain a second extract, (vii) comparing and/oranalyzing the target molecule contained in the ligand-immobilized solidphase carrier first extract and the target molecule contained in theligand-immobilized solid phase carrier second extract, and (viii)identifying the target molecule as being specific for the ligand if thetarget molecule is detected in the ligand-immobilized solid phasecarrier first extract and not detected in the ligand-immobilized solidphase carrier second extract, or detected in the ligand-immobilizedsolid phase carrier second extract at a significantly lower level thanin the ligand-immobilized solid phase carrier first extract.
 2. Themethod of claim 1, wherein the inert substance is stearic acid.
 3. Themethod of claim 1, wherein the inert substance is structurally similarto the ligand, has non-specific absorption and does not possess thephysiological activity possessed by the ligand.
 4. The method of claim1, wherein the sample is a biological sample.
 5. The method of claim 1,which further comprises calculating the binding constant of the targetmolecule binding to the ligand.